Cave adaptation has evolved repeatedly across the Tree of Life, famously leading to pigmentation and eye degeneration and loss, yet its macroevolutionary implications remain poorly understood. We use the North American amblyopsid fishes, a family spanning a wide degree of cave adaptation, to examine the impact of cave specialization on the modes and tempo of evolution. We reconstruct evolutionary relationships using ultraconserved element loci, estimate the ancestral histories of eye‐state, and examine the impact of cave adaptation on body shape evolution. Our phylogenomic analyses provide a well‐supported hypothesis for amblyopsid evolutionary relationships. The obligate blind cavefishes form a clade and the cave‐facultative eyed spring cavefishes are nested within the obligate cavefishes. Using ancestral state reconstruction, we find support for at least two independent subterranean colonization events within the Amblyopsidae. Eyed and blind fishes have different body shapes, but not different rates of body shape evolution. North American amblyopsids highlight the complex nature of cave‐adaptive evolution and the necessity to include multiple lines of evidence to uncover the underlying processes involved in the loss of complex traits.

中文翻译：

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使用系统基因组学和几何形态计量学推断北美弱视鱼类的洞穴适应进化

洞穴适应在生命之树中反复进化，以导致色素沉着和眼睛退化和丧失而闻名，但其宏观进化的影响仍然知之甚少。我们使用北美弱视鱼类，一个跨越广泛洞穴适应的家庭，来研究洞穴专业化对进化模式和节奏的影响。我们使用超保守元素位点重建进化关系，估计眼状态的祖先历史，并检查洞穴适应对体形进化的影响。我们的系统发育分析为弱视动物进化关系提供了一个有充分支持的假设。专性盲洞鱼形成一个进化枝，洞穴兼性有眼弹簧洞穴鱼嵌套在专性洞穴鱼内。使用祖先状态重建，我们发现对 Amblyopsidae 中至少两个独立的地下殖民事件的支持。有眼鱼和盲鱼有不同的体型，但体型进化的速度没有不同。北美弱视动物突出了洞穴适应进化的复杂性，以及包括多条证据以揭示复杂性状丧失所涉及的潜在过程的必要性。